9MEY | pdb_00009mey

Crystal structure of RIT1(GDP) bound to LZTR1(Kelch domain)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 
    0.256 (Depositor), 0.255 (DCC) 
  • R-Value Work: 
    0.217 (Depositor), 0.217 (DCC) 
  • R-Value Observed: 
    0.219 (Depositor) 

Starting Models: experimental, in silico
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Structural basis for LZTR1 recognition of RAS GTPases for degradation.

Dharmaiah, S.Bonsor, D.A.Mo, S.P.Fernandez-Cabrera, A.Chan, A.H.Messing, S.Drew, M.Vega, M.Nissley, D.V.Esposito, D.Castel, P.Simanshu, D.K.

(2025) Science 389: 1112-1117

  • DOI: https://doi.org/10.1126/science.adv7088
  • Primary Citation of Related Structures:  
    9MEY, 9MEZ, 9MF0, 9MF1

  • PubMed Abstract: 

    The RAS family of small guanosine triphosphatases (GTPases) are tightly regulated signaling molecules that are further modulated by ubiquitination and proteolysis. Leucine Zipper-like Transcription Regulator 1 (LZTR1), a substrate adapter of the Cullin-3 RING E3 ubiquitin ligase, binds specific RAS GTPases and promotes their ubiquitination and proteasomal degradation. We present structures of LZTR1 Kelch domains bound to RIT1, MRAS, and KRAS, revealing interfaces that govern RAS isoform selectivity and nucleotide specificity. Biochemical and structural analyses of disease-associated Kelch domain mutations revealed three types of alterations: impaired substrate interaction, loop destabilization, and blade-blade repulsion. In cellular and mouse models, mutations disrupting substrate binding phenocopied LZTR1 loss, underscoring its substrate specificity. These findings define RAS recognition mechanisms by LZTR1 and suggest a molecular glue strategy to degrade oncogenic KRAS.


  • Organizational Affiliation
    • National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GTP-binding protein Rit1
A, C
197Homo sapiensMutation(s): 0 
Gene Names: RIT1RIBBRITROC1
EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for Q92963 (Homo sapiens)
Explore Q92963 
Go to UniProtKB:  Q92963
PHAROS:  Q92963
GTEx:  ENSG00000143622 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ92963
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Leucine-zipper-like transcriptional regulator 1
B, D
322Homo sapiensMutation(s): 0 
Gene Names: LZTR1TCFL2
UniProt & NIH Common Fund Data Resources
Find proteins for Q8N653 (Homo sapiens)
Explore Q8N653 
Go to UniProtKB:  Q8N653
PHAROS:  Q8N653
GTEx:  ENSG00000099949 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8N653
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free:  0.256 (Depositor), 0.255 (DCC) 
  • R-Value Work:  0.217 (Depositor), 0.217 (DCC) 
  • R-Value Observed: 0.219 (Depositor) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 148.582α = 90
b = 148.582β = 90
c = 130.728γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United States75N91019D00024

Revision History  (Full details and data files)

  • Version 1.0: 2025-09-10
    Type: Initial release
  • Version 1.1: 2025-09-24
    Changes: Database references